Declining crop productivity and environmental pollution are two key issues associated with sustainability of rice-wheat system in Nepal. The former one is related to declining soil organic matter and shortage of water as well as laborer; whereas, the latter is due to emission of greenhouse gases (GHGs) from this system. This article reviews the potential of soil conservation practices, especially organic matter and zero-tillage, against these two issues in rice-wheat system of Nepal. Farm Yard Manure (FYM), compost and green manure are the major sources of organic matters in rice-wheat system in Nepal. The organic matter improves the physical, chemical and biological properties of soil; and contributes in minimizing GHG emission. Adoption of biogas technology, improved FYM/compost and spring season green manure crops hold enormous potential to minimize GHGs emission from rice-wheat system. Similarly, zero-tillage reduces the cost of cultivation, allows early planting of wheat, reduces water requirement and increases the crop yield by 16-50 % as compared to conventional tillage. This practice also reduces the consumption of fossil fuel (up to 64 %) by reducing the tillage requirement, and minimizes the oxidation of soil organic matter, thereby contributing in the GHGs mitigation. The other options contributing to the above two issues are water, land, and fertilizer management, and upland rice varieties. This review shows that the integration of the above options would contribute in sustainability of the production system and environmental but more understanding is needed regarding the applicability of the zerotillage using seed drill in wheat under different geographical and socio-economic contexts of Nepal given the limited studies available.